iqtlabs / squiggle

📈 DNA Sequence Visualization for Humans

This repository has moved to https://github.com/Benjamin-Lee/squiggle

Squiggle is a two-dimensional DNA sequence visualization library that can turn FASTA sequence files like this:

>lcl|NC_000011.10_cds_NP_000509.1_1 [gene=HBB]
ATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAG
TTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGG
GGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGT
GCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACT
GTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCA
TCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAAT
GCCCTGGCCCACAAGTATCACTAA
>lcl|NC_005100.4_cds_NP_150237.1_1 [gene=HBB]
ATGGTGCACCTGACTGATGCTGAGAAGGCTGCTGTTAATGGCCTGTGGGGAAAGGTGAACCCTGATGATG
TTGGTGGCGAGGCCCTGGGCAGGCTGCTGGTTGTCTACCCTTGGACCCAGAGGTACTTTGATAGCTTTGG
GGACCTGTCCTCTGCCTCTGCTATCATGGGTAACCCTAAGGTGAAGGCCCATGGCAAGAAGGTGATAAAC
GCCTTCAATGATGGCCTGAAACACTTGGACAACCTCAAGGGCACCTTTGCTCATCTGAGTGAACTCCACT
GTGACAAGCTGCATGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACATGATTGTGATTGTGTTGGGCCA
CCACCTGGGCAAGGAATTCTCCCCCTGTGCACAGGCTGCCTTCCAGAAGGTGGTGGCTGGAGTGGCCAGT
GCCCTGGCTCACAAGTACCACTAA

into gorgeous, interactive visualizations like this:

(Click the picture to view an interactive version.)

Installation

If you don't have Python 3.5 or greater installed, be sure to get it. To get the current stable version of Squiggle, run:

$ pip install squiggle

Or, alternatively, if you want to get the latest development version:

$ pip install git+https://github.com/Lab41/squiggle.git

Usage

Using Squiggle is as easy as:

$ squiggle your_sequence.fasta

Squiggle has tons of options available to make beautiful, interactive visualizations of DNA sequences. To get a full rundown of the various option, take look at the documentation here.

Citation

Using Squiggle in your research? Please cite it!

• Lee, B. D. (2018). Squiggle: a user-friendly two-dimensional DNA sequence visualization tool. Bioinformatics. doi:10.1093/bioinformatics/bty807

@article{Lee2018,
  doi = {10.1093/bioinformatics/bty807},
  url = {https://doi.org/10.1093/bioinformatics/bty807},
  year  = {2018},
  month = {sep},
  publisher = {Oxford University Press ({OUP})},
  author = {Benjamin D Lee},
  editor = {John Hancock},
  title = {Squiggle: a user-friendly two-dimensional {DNA} sequence visualization tool},
  journal = {Bioinformatics}
}